Congenital diaphragmatic hernia (CDH) is a common birth defect with a prevalence of 1 in 3000 live births, constituting 8% of all birth defects. Many cytogenetic abnormalities have been associated with CDH, and evidence is accumulating that many developmental defects can result from small genomic alternations invisible at the cytogenetic level, resulting in changes in copy number of contiguous genes. We hypothesize that in some proportion of cases of birth defects, including CDH, these genomic alternations may be mosaic and may not be readily detectable by testing lymphocytes in blood. We propose to identify changes in gene copy number by analyzing diaphragm tissue and other tissue from patients with CDH, using genome wide oligonucleotide microarrays to perform high resolution gene copy number assessment. Our long-term goal is to define a set of novel genomic aberrations important in the etiology of CDH, characterize new syndromes associated with CDH, and identify new genes implicated in diaphragm development. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information that can improve genetic counseling. We will accomplish this through the following specific aims: 1) Obtain diaphragm, skin, blood, and when possible amniotic fluid samples from 250 neonates with CDH, 100 children with previously repaired CDH, and amniotic fluid on 250 cases of fetuses with prenatally diagnosed CDH and their parents for oligonucleotide microarray copy number analysis; 2) Analyze the diaphragm (neonatal), blood (pediatric) or amniotic fluid (prenatal) samples for copy number changes (CNCs) using high density oligonucleotide microarrays, filter out benign copy number polymorphisms, and determine if CNCs are de novo by comparing parents and offspring and determine tissue mosaicism; 3) Identify recurrent CNCs, define the minimal overlapping interval, identify all the genes in the minimal interval of the recurrent CNCs, and sequence positional/physiologic candidate genes and determine if there are overlapping clinical features among patients that can be used to define a genetic syndrome with associated clinical features and prognostic implications; and 4) Correlate results of genetic analyses and survival to discharge and 2 years of age, associated birth defects, severity of pulmonary hypertension at 1 and 3 months, weight and height at 2 years, and Bayley Scales of Infant Development-II and Vineland Adaptive Behavior Scale at 2 years in cases of neonatal ascertainment. PUBLIC HEALTH RELEVANCE: Congenital diaphragmatic hernia (CDH) is a common birth defect with a prevalence of 1 in 3000 live births, constituting 8% of all birth defects. Our goal is to define a set of novel genetic aberrations causing CDH, characterize new syndromes associated with CDH, and identify new genes implicated in diaphragm development. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information for patients and families with CDH.